Broken Yet Whole
by c0l0r-bl1nd n355
Summary: What will you do when everything is taken from you? Will you give up just to end the pain? Or will you continue to end other's pain? Shinji rejects instrumentality to redo his life. He chooses to also bring back Asuka and Rei. How will they deal with the pain? Will they seek shelter in each other? *Pairing later on.* *rated M just in case*
1. Chapter 1: What Shall Not Be

**A/N: heya peoples... hows it been?**

 **well, this is the newly updated version, if you like the first better than just write me at " c0l0r.b1nd.n355 " and type 'hell Yeah' if you like this version or 'fuck no' if you want me to reupload the original.**

 **Here comes "Broken Yet Whole" version 2.0**

 **please enjoy and don't hold back on the reviews. Thanks.**

* * *

 _ **Chapter 1: What Shall [Not] Be**_

* * *

They came one by one at first and later by the dozens. The not-children held them back while they could. As the years past, the boy saw less and less of his friends and partners as they were killed off one by one during the waves of Angels.

The first to die was Touji. Shinji was forced to kill him by his father... no, not his father, father was a name he had not earned yet... the Commander. The Commander forced Shinji to kill Touji when his Evangelion was taken over by one of the Angels.

The second to die was Misato. She was killed by the last Angel, mankind. Nerv was prepared and could defend itself from the Angels, but it was not prepered for attacks from itself. In the end, mankind's only true enemy was itself. That's why mankind was dubbed the last true Angel. Misato ended up being shot by an invading force of humans.

The third to die was Asuka; she was killed by the Mass Production Evangelions when she trying to protect Shinji and Rei.

Mari died shortly after when Nerv was attacked by The Angel Of The Morning. Rei died for the second time by blowing up the Angel with a N3 missle.

The last of Shinji's friends to die was the second to last Angel, Tabris, formerly known as Kaworu. He had Shinji end his life after he found out that The Angel In Central Dogma was in fact, Lilith, not Adam as SEELE thought.

Shinji held out with Rei III by his side for four more years, fighting off the Angels which came back endlessly. The two young adults knew nothing of life outside of fighting Angels.

In turn, it was person on the inside which cause the Third Impact to start. The Commander ejected Rei III out of Unit 00, and she was crushed by the Angel.

Rei the fourth was born, and she was brought to Lilith before her memories had surfaced.

The Third Impact commenced.

* * *

 _Setting: The Sands of Time of The LCL Sea_

* * *

Shinji woke up to the sound of silence. He sat up, brushing the sand off of the side of his face. He looked around at his surroundings. From what he could tell, he was standing on a black sand beach facing a sea that looked like the liquid that was inside of the entry plug of the Eva units.

 _ **What do you seek, Lilin?**_ A Voice echoed around him, seeming to come from everywhere and yet nowhere.

 _I remember that word, Lilin, Kaworu once called me a 'Lilin'._ Shinji thought.

"What do you mean, 'What do I seek?'" Shinji replied.

 _ **You are The Chosen, you are The Medium,**_ The Voice said back, amusingly. _**I am allowed to give you anything, but only ONCE, Godchild.**_

"Can you at least show yourself, because I really don't feel comfortable talking without looking at something." Shinji asked nervously.

The Voice seemed to pause, _**Is that what you want?**_

"Can you at least just show yourself as a favor?" the boy pleaded.

 _ **Fine...**_ with that, the Voice showed itself. It became first an outline and then the figure of a person.

Shinji recognized the figure in which the Voice had chosen to show itself as.

"Rei?" Shinji asked softyle. "No, it can't be..." he shook his head, then talking to himself. "She merged with The Gaint." The boy looked up at Rei look-alike. "Lilith?" He asked.

 _ **Very well, Godchild. I am Lilith.**_

"Why do you keep calling me Godchild?" he asked.

 _ **You did hold off waves and hordes of Angels for four years, even after your friends died off. You defied the Gods for four years. In the end, it was your own kind that betrayed you. So, it is fitting to call yourself Godchild.**_

Shinji sat down in the sand. "So, you said that you are able to give me anything I want, but only once, right?" he queistoned The Woman.

 _ **Yes**_

"So, can you bring Rei, Asuka, and me back in time so that we can have another chance to make peace?"

 _ **Yes and no,**_ The woman sighed, _**I can bring all three of you back, but I would have to relocate all of you to another timeline in which it would not interfere.**_

Shinji jumped up, "Then can you do it?"

 _ **I will bring all of you back, but first you all need to train and you need to learn the Angelical language if you want to try to make peace with the Angelkind.**_

And the training commenced.

* * *

 **A/N: So, how was it? Better? Worse? Please let me know!**

 **Until next time, stay healthy, fit, and depressed!**


	2. Chapter 2: Through The Abyss Of The Past

**A/N: So, I'm back for another chapter of "Broken Yet Whole". **

**Thanks** Hellsink Bathhall **for your review. I really appreciate it.**

 **I'm trying to push for longer chapters but the work is very tedious. I'll try though. *No promises. xD**

 **Well, enjoy..If possible.**

* * *

 **Chapter 2: Through The Abyss Of The Past**

 _Part One: Inside Those Crimson Eyes_

 _REI'S POV_

Several years ago, before The German was told she was a pilot, Rei was told that she herself was a clone. The man that told her was trustworthy at the time. So, she believed him, even trusted him.

She was told she was a clone of The Third's Mother, Yui Ikari. The Commander, however, saw her as an imperfect copy. In reality, she was a perfect copy, of The Angel In The Dark, Lilith.

She went through many trials and had overcome many hardships. There was no problem because she was told emotions held people back and hurt themselves and others. In response to that, she severed all emotions and walled them up in the pits of her soul.

She always knew that she was more than she seemed, that there were more secrets inside of her than The Doctor and The Commander wanted her to know. She had many quiestons that she wanted answers. In turn, she locked the quiestons up too.

Nobody would answer her quiestons so she decided to find the answers herself. The Doctor showed her how to code, so Rei created programs that reproduced and infested every corner of The Headquarters. She had access to every secret of everybody, the answers to the quiestons she had and more since she was denied those answers.

She was snooping around one day when she came across something that intrigued her. She had found a newly created folder dubbed "Third Child". She knew The Third had to exsist since there were three EVANGELIONS in exsistance: one in Germany and two right there in Japan. Rei had already found out everything there was to know about The Second, a fiery red-haired girl, around her 'Age', by the name of Asuka Langley Soryu.

She dug through the files, copying them to a fresh hard-drive as she went, learning more and more of The Third.

Among the information she found out about The Third, there was The Age (around her 'Age'), current living (At The Second's manor in Germany), birthplace (Japan, same as "Rei's"). She also found out that His Name was Shinji Ikari, he was The Commander's son, and he had brown eyes and hair.

How Interesting.

One emotion broke free of the previously tight bond: a deep Curiosity followed by Interest.

Rei decided that she was going to find out more about the boy when he came back home.

 _Part Two: Inside That Broken Doll_

 _ASUKA'S POV_

The first time she met the boy was when she was six. He was sent over to the manor by his father. She later found out that his name was Shinji of the Ikari family. He was the only person that she could trust or even talk to. Over the years, they became really close, until she had to leave.

When she was ten, she was told she was The Second Child, The Pilot of Evangelion Unit 02. So, she went away for special training to become one of the protectors of man.

Asuka never saw Him again for years, until the Angels came back and she moved to Japan.

 _Part Three: The Void of Hurt_

 _SHINJI'S POV_

He was a broken person. Not the normal type of broken, but the type that involved mental neglect and abuse. When he was younger, he had seen his mother die in front of his eyes. Two years later, his father left him and sent him to Germany. There he was bullied and abused until The Second helped him. When he found out that he was The Third, he thought that maybe he now had something to live for. He piloted not for his sake, but for the sake of others. Later, that ends up not only hurting him, but hurting others as well.

When he met Asuka, he was being beat up by a gang of kids older than him outside of the Academy. Thier excuse was that he did not fit in because he was a foreigner. While they abused him, they told him that he would never belong anywhere. He knew they were right.

Then Asuka showed up. She fought the boys and almost broke their jaws in the process. She held out her hand and helped him off of the ground. "Komm schon, Idiot." She said. Come on, idiot.

 **A/N: Sorry if the translations aren't great.**

 **My German isn't that great.**


	3. Chapter 3: Lay Right Here The Returned

**A/N: Song of the chapter:**

 **Sometimes you wake to see yourself Take happier pills to keep you well And sometimes you talk to hear yourself Screaming out loud.**

 **Never ever heard a word you said. Can't you see yourself? Can't you understand?**

 **There's more truth in the way that you lie. But you take a stab at all that's surrounding your mind.**

 **Can't you sweep this shit to the side.**

 **It's so fucking nice to have you here To turn our lives from what we fear But sometimes you're worthless and weak and alone**

 **Will you ever grow? Here I am I want to help you out**

 **Can't you see yourself? Can't you understand?**

 **There's more truth in the way that you lie So you take a stab at all that's surrounding your mind**

 **Well you won't believe when this cloud lifts what you might find. You'll find it's all over and can't you see it's all over**

 **This face that stares back at you Stares back at you, from these happy pills They won't keep you well tonight**

 **I'll be here to watch you shudder**

 **I'll be the one that holds you under**

 **Every time you try to shift it**

 **Every time your stitch is slipping**

 **Slipping through time**

 **There's more truth in the way that you lie. So you take a stab at all that's surrounding your mind**

 **Well you won't believe when this cloud lifts what you might find**

 **Got it all over you now**

 **Got it all over you now**

 **Got it all over this**

 **The face that stares back at you from these happy pills They won't keep you well tonight**

 **-Happy pills by candlebox**

 **::::::: :::::::**

 **Kind of speaks for this type of anime, right?**

Chapter 3: Lay Right Here/The Returned

 _Before The Return_

The Angel turned to Shinji. **"While you were asleep, I fused a piece of myself inside of you. The same applies to the others."** She cocked her head. **"Your Angelic Anti-Terror Field should blocked it out, along with the AT Field that surrounds your heart."**

Lilith turned and faced the three. **"Remember, try not to do anything rash, because you risk losing control and showing your Angelic side. Such' ihn über'm Sternenzelt!**

 **Über Sternen muß er wohnen."**

Lilith kneeled down on the ground. **"Come and help me, little ones, open The Gate so that you may travel back into the next timeline."**

Shinji, Asuka, and Rei kneeled down beside her, and they opened The Gate.

::::::::::::::::::::

 _Current Time_

 _Tokyo III_

Shinji opened his eyes in the next moment and found himself back in what looked pretty much like the past Tokyo III. The alarms had finally stopped ringing. For over twenty minutes those blasted things and their high pitched ringing had aired followed by a pre-recorded message. A standard issue message informing citizens to remain calm and seek shelter.

The Angel-Child had to make sure that he had come back. He jogged over to the phone booth and picked up the phone. Sure enough, a voice echoed from the speaker: _~~ "We're sorry. Due to the state of special emergency, no lines are currently available. This is a recorded message." ~~_

He sighed in relief. Now all he had to do was wait for Misato to arrive.

He leaned up against the side of the phone booth and plugged in his earbuds. As The Moonlight Sonata played, he tapped out the notes on his leg.

He heard the screeching of attack chopters being ripped apart close-ish by, followed by the sound of the explosion as they crashed into each other. However, this did not faze Shinji as he had gotten used to the sound of chaos.

Shinji heard a car engine being forced to greater speed that it should be. He took out his earbuds and shut the SDAT off and stuffed them into his pocket.

Looking toward the sound, he saw the blue car speeding towards him. The car soon skidded to a halt as the driver angled the vehicle so that the passenger door was facing Shinji. The door quickly opened from inside, and Shinji saw a woman with dark hair holding it open, leaning over the center console while wearing a red jacket over a black shirt. "Shinji Ikari, right?" the woman asked him.

Shinji jumped into the car, quickly slamming the car door behind him. "Just drive, I can introduce myself to you later. I'm sure you want to hear my whole life story." He said with a smart remark.

...

 _Meanwhile at Nerv Headquarter's_

Looking at the static screen, the JSSDF generals all began congratulating themselves on a job well done against the Angel. One of them looked up at Ikari and Fuyutsuki with a smug smirk on his face. "Well, Commander Ikari, it seems that we won't be needing your help after all," the general said.

Gendo said nothing. He merely pointed a gloved finger toward the screen as it cleared. "I-Impossible!" another general said, causing the first one to turn around and gasp in shock. On the screen, The Angel of The Morning stood amidst the flaming remains of the countryside. Its bird-like mask had been cracked, and it had burn marks all over it, but as its flesh bubbled and simmered, a new mask began to grow underneath the old one, eventually pushing it out of the way before It reached up and gingerly removed the old mask from his face, dropping the cracked shell onto the decimated forest floor below.

"It... it just regenerated itself. Healed its wounds like nothing had even happened," one general said in complete awe.

"That's it, then. The N2 mine was our last resort," one particularly shaken general said.

"Wait, couldn't we just drop another one onto it? It seemed to be injured by the first one," one optimistic general suggested.

"No. We'd need to drop a hundred mines onto that thing. Plus, with the way that thing can regenerate itself, it would be pointless, and far too destructive," another general said in response.

The highest ranking of the generals, General Kisuke Hikawa, turned around to look at Gendo and Fuyutsuki. "Gentlemen... this operation is now under the jurisdiction of NERV," Hikawa said reluctantly.

Gendo, his face obscured by how he had his hands postured, smirked. "Of course, General. After all, this is what NERV is for," he said.

Hikawa sighed in response. "Lets hope that these... toys of yours can do a better job than we did," he said begrudgingly. Gendo smirked subtly from behind his gloved hands.

...

Misato pulled up through the Emergency Tunnel. A squad of guards surrounded the car as the leader went to Misato's open window. Weird, Shinji thought, This was not like this before. It must be because of the changed timeline.

"We need to see ID." The Leader said in a stern voice. Misato pulled out her card and showed it to the man while Shinji dug around in his pocket.

After finding what he was looking for Shinji pulled out his ID and the letter from Commander Ikari. A simple one word summoning 'Come' that he remembered scaring the shit out of him when he was a child. He showed the man the ID and he gave the letter to Misato "I suppose you want this?" He asked while presenting it.

After the man had seen his ID, he gave it to Misato.

She took a quick glance at it, absorbing all of the info on the page, only raising an eyebrow at the mostly destroyed letter from the Commander with a short comment of "Just like mine." before she moved on to the ID whilst making sure it was verified and after looking at it for a little while she passed it back over with another cheery grin and a nod.

"Kid, what's with the scar?" Misato asked as she noticed a long scar on the side of his hand while the car traveled down the car-train.

"Which one." Shinji answered on reflex, so used to questions about them that he forgot that he wasn't supposed to have the many scars he had gained through the link with his Eva.

"You have more?" Misato tried to keep the concern out of her voice, not wanting to sound condescending but if the Third Child was abused then it could cause problems, this aside from her personal hate of child abusers.

Seeing the look on his face she decided to drop it and bring it up later she set another grin on her face and turned to Shinji. She looked at something beside him.

The Third looked out of his window and noticed the scenery. "Nice, a Geofront!" He exclaimed, noticing that the Geofront was different than before. Now the NERV pyramid was fully surrounded by a dome and the dome had what looked to him as retractable panels that might move aside to allow anti-angel weapons to push out.

Misato noticed the boy's partial excitement. _So, he likes the military,_ she thought to herself.

...

 _Ritsuko Akagi's POV_

 _~~"Would the head of Project E, Technical Department Division 1, Dr. Ritsuko Akagi,"~~_ A voiced buzzed over the intercoms, _~~"please contact Captain Misato Katsuragi of Operations, Division 1, immediately."~~_

Ritsuko climbed out of the LCL lake, and starting changing. "I don't believe it. She got lost again, didn't she?" she sighed.

…..

The elevator was showing that they had just reached floor B-28. The elevator stopped and the doors slid open to reveal a waiting Ritsuko.

"Uh, hiya, Ritsuko." Misato stammered.

The Blonde doctor pushed her way into the elevator. The doors slid shut.

"What were you doing, Captain Katsuragi?" she asked, "We're short on both time and manpower, you know."

Misato bowed slightly. "I'm sorry." she said sheepishly. Ritsuko sighed.

"So this is the boy?" she asked The Captain.

"Right. According to the Marduk report, he's the Third Child."

Ritsuko turned to him, "It's nice to meet you."

Shinji looked up at the doctor, "Sure." he replied, coldly.

Misato looked at Ritsuko with a type of understanding, "he's just like his father. Like how he's unendearing."

Shinji's blood ran both hot and cold with that statement. "I am NOTHING like that piece of trash!" he exploded,memories rushing at him of everything the Commander had done to him and the others in his past life, "Why do you think that i have been away for so long?!"

With that, both of the women fell silent.

...

As the platform rose diagonally, the women starting talking about Unit 01. Shinji stayed silent, knowing that he was not supposed to know about what they were talking about.

After a little bit, their platform rose to meet the floor.

The room opened up to a very huge area, with Unit 01 in the very middle of it. As the small group stood on one of the columns, Gendo looked down.

The Commander of NERV held no emotion as he spoke towards his son. He was, however, taken aback to see that his son didn't even flinch or awe or… do something at the sight of the biological behemoth in front of him.

"Shinji. It's been a…" His words died in his throat as his son emotionlessly strode onto the scaffold which led to the Entry Plug.

"Hand me the Neural Clips, and hurry up. There's no time to waste." Shinji said, feigning ignorance of his father's words, and holding his hand out to a technician near the Plug. The technician handed Shinji the A10 Neural Clips, and Shinji threw the headpiece on, before sitting in at the helm.

...

A couple minutes later

Shinji is sitting in the entry plug

"Doc-DOCTOR! Come and have a look at these Sync Rate readings!" Shigeru Aoba reported to Ritsuko Akagi. She rushed to the screen readings and adjusted her glasses.

"I'm… I'm seeing things, aren't I?" She whispered to herself. Gendo viewed the screen from afar, like a hawk, and inwardly balked at his son's synchronicity with his EVA.

"It's… jumping from 900% to 1000%." Makoto Hyuga said, double-checking his co-worker's monitor.

"And no damn Plugsuit!? Are you sure our readings aren't off!?" Maya Ibuki asked, trying at first by herself to locate the source of any bugs in the NERV systems.

"Get me a visual of the cockpit, NOW!" Ritsuko yelled, and as the dull screen showed itself, her heart leapt in her chest. _(well..fuck me in the ass and call me daddy.. she thought)_. Shinji was staring directly out of the eyes of the EVA – they had reached beyond perfect sync, without the young boy dissolving into the life-giving waters of LCL.

His eyes were green, just like 01's, and every twitch of skin he made, the EVA mimicked perfectly. As Shinji was drawn out of his trance, the Sync Rate dropped dramatically, and he lurched forward to catch his breath in the flooding container of LCL.

"Shinji! Pilot Ikari, come in!" Misato gained contact with Shinji once more, and noticed him stir. He smiled at the screen and chuckled.

"Let's get to it. Send everything else back, they'll only get in the way!" Shinji demanded, as it was as much as he could do. The EVA pilot decided that any unnecessary deaths were just that – unnecessary. He would save all that he could.

::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

 **A/N: And, that's it for this chapter.**

 **next chapter will be the fight between shinji and the angel of the morning.**

 **S.T.U.N.T.! (Stay Tuned Until Next Time!)**


	4. Chapter 4: In The Pain of The Morning

**A/N:**

 **Sorry for the long wait. at the time that I am writing this, it is been 5 weeks, 1 day, and 30 something minutes since my last update. I have been busy with schooling and other projects. I have been working on couple other books, I'll publish when i have at least a few chapters done so i won't be too bogged down.**

 **Well, anywho...here's the**

 **Song Of the Chapter:**

 **"An die Freude"**

 **Freude, schöner Götterfunken,**

 **Tochter aus Elysium,**

 **Wir betreten feuertrunken,**

 **Himmlische, dein Heiligtum!**

 **Deine Zauber binden wieder**

 **Was die Mode streng geteilt;**

 **Alle Menschen werden Brüder**

 **Wo dein sanfter Flügel weilt.**

* * *

Chapter 4: In The Pain of The Morning

* * *

Shinji awoken to find himself staring at a blank, white ceiling. Where am I? the boy thought to himself. He sat up and looked at his surroundings. Suddenly, his arms and head bursted in pain. And then the memories overtook him.

:::::::::SCENE CHANGE:::::::::

 ** _Earlier_**

The gravity pushed him down into the seat as the Eva was launched upwards at neck breaking speeds up the elevator specially built for the False-Gods.

The Eva slammed into the top of the shaft and the arm-locks unlatched.

 _~~"Shinji, try to walk."~~_ Misato ordered the boy. However, Shinji lunged forward towards the angel.

He reached to his shoulder and pulled out the Progressive Knife.

...PERSPECTIVE CHANGE...

The Angel of The Morning looked up at the Being that rushed at him. _That's weird_ , he thought, _Why is it running at me, it's brethren...Wait a minute, that's a false being!_

 _Abomination!_ The Angel screamed as ran towards the Eva, _False duplicate of The Father!_

Shinji heard these things and replied back through the Angel Network. "Sachiel! Listen to me!" he thought-screamed. I'm here to liberate you from Father Adam!"

Hearing no reply, the God-Child grabbed Sachiel and stabbed him in the face and holding him down with his Anti-Terror Field.

 _ **Rip out the core and eat it**_

Shinji heard the voice echo in his head. It took him a second, but he realized that it was the part of Lilith that She had merged with him.

He proceeded as he was told and cut the core out with the Knife. He looked and saw that there was a Person, at least it looked like one, in the center of the core. Shinji ate the core around the person and cleaned the Guy off.

The Angel fell to the ground and erupted into a blue cross made of pure energy as Shinji climbed down the shaft.

He placed the guy on the walkway and spoke into the comm. "There's a male here that needs medical attention." Then Shinji passed out.

:::::::::SCENE CHANGE:::::::::

 _ **Current Time, NERV Hospital**_

Shinji woke back up from his daze, finding Ritsuko standing in the doorway. "Your father wants to see you." She ordered him, pondering on what had happened earlier.

"Don't call him that, I'll be there in a moment." he climbed out of bed, after a minute, noticing that he was just wearing a hospital gown. The Doctor handed him a pair of clothes.

"I thought you might need these."

::::::::::

Shinji walked down the hall, noticing that there was a lot of graffiti on the walls. On the wall to the left was the logo of SEELE, with 'Überm Sternenzelt richtet Gott, wie wir gerichtet' scrawled hastily underneath the picture. On the opposite wall was the NERV logo, a half leaf with 'NERV' painted near it, with 'God's in his heaven, all good in the world' scrawled neatly around it in an arc. Kind of Ironic, since of the past.

As he entered the room that occupied what Gendo called an office, he noticed The Commander sitting at a desk with his hands folded in front of him, trying to be intimidating. Well, that was what Shinji thought he was trying to do, obviously failing.

He approached the desk **, "You wanted to see me?"** he growled, not trying hiding the bitterness and anger in his voice.

Gendo looked visibly shook, before he fixed himself and answered, "Yes...Do you know anything about what had happened earlier?" He questioned the boy that should've been a cowardly bitch since of the preceding circumstances. Instead, he seemed to be even more of an ass than even he was. Gendo decided to make a note of this.

Shinji decided to play the role of the fool. "I don't know what you are talking about."he said, mocking The Commander.

"God damn, you know what I'm talking about!" Gendo yelled breaking.

Shinji shook his head in mock pity. "Maybe you was just hallucinating, that'll explain a lot." he countered with a smirk.

"Don't test me child."

Shinji sighed. "If you really want to know," he started, moving closer to Gendo until he was at his ear, "Come over for dinner at Misato and My place, since that's where I'll be living at because i want to be as far away as possible from you." he whispered. " **By the way, you tell anyone about what we've talked about, fuck having anybody else do it, i'll personally track you down and rip out whatever fucking heart you have and literally make you eat it."** he continued menacly.

Gendo swallowed and his hands started to shake.

"Okay."

Shinji turned and started walking away, "Bye _Father_." He said, leaving the room.

:::::::::SCENE CHANGE:::::::::

Misato tried to catch up with Shinji, "Hey...Wait up…" she gasped while trying to catch her breathe. Shinji stopped walking and waited for The Captain to catch up.

"Yes?"

"I was wanting to talk to you about your living arrangements." she panted.

"Don't worry, i've sorted it out with Gendo himself." as he said that, he could see Misato's face visibly drop in disappointment. "I'll be living with you."

"Yay!" she jumped in glee, cheering up real quick. "Let's head home."

:::::::::SCENE CHANGE:::::::::

Misato and Shinji walked into the apartment and he noticed how messy the room was, just like it was in the past lifetime. "Verdammt…" Shinji sighed. "You're going to help me clean later."

Shinji pulled out a chair from the table for Misato and one for himself. Misato sat in the seat and giggled, "You're a real gentleman, Shinji." then she got serious. "By the way, you said you were going to explain about what happened earlier."

Shinji settled down in the seat. "You might want to grab a beer before I start." Not even stopping to question him about what he said, Misato decided to just grab a beer from the fridge. When she got back to the table, she found that Shinji had grabbed a bottle of Bacardi 151 out of her hidden storage.

:::::::::SCENE CHANGE:::::::::

"There's no fucking way," Misato started to laugh. "You must be joking."

Shinji waited for a few more minutes before glaring at her. **"Are you fucking done?"** he said quietly, making her notice him even more. When she finally quieted down, he continued, breathing shakingly. "I should of known that you wouldn't believe me the first time around."

The Third Child stood up. "I guess I have to show you." He proceeded to take of his shirt, a chiseled body etched with massive scars. He closed his eyes and breathed inwards before expelling it. Pure white wings burst out of his shoulder blades, shocking the purple haired guardian. "Just like before…" she said before collapsing.

"Shit, I forgot that she witnessed The Second Impact." he furled up his wings back into his body and picked her up, carrying her to her room and laying her down on her bed. "I'll explain more when you wake up…" he muttered as he pulled the covers over her, not wanting her to be cold.

* * *

 **A/N:**

 **Hope you enjoyed another chapter, trying to work towards them being longer.**

 **Until next time folks.**


	5. Chapter 5: Mistaken Identities

**A/N:**

 **Did ya like the previous chapter? if so, I can't wait to read them delicious reviews.**

 **If not, oh well, be kind enough to tell me what was wrong doll...**

 **Song of the Chapter:**

 **ha I'm not given you any lyrics this time... so off you go to do some research**

 **here it is:** **everybody dies in their nightmares by xxxtentation**

 **works perfectly with how I'm trying to pull this book towards..**

 **i'll try to keep the errors down low...**

 **if ya'll would like specific Evangelion one shots, fell free to PM me, I'll get them wrote when i have the chance...Probaly sooner than the next chapter since one-shots aren't hard to write. oh, and I'm in the process of writing another story "Wandering Souls", 'nother EVA story.**

 **welp, time for the promised chappy**

 **luv ya... pleasant reading**

* * *

Text Guide:

 _ **"Spiritual Dialogue"**_

"Regular Dialogue"

'Thoughts (may be updated in the future)'

 **Emphasized** **Dialogue**

 **(A/N)**

 _~Electronic Voices~_

 _/ scene change for now_

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Chapter 5: Mistaken Identities

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Shinji opened his eyes to find himself in a clearing in a thickly wooded forest. He closed his eyes and rubbed them before accepting that he was not asleep, or at least he must be lucid dreaming. **(A/N: By the way, check out Lucid Dreams by Juice Wrld)**

The Third Child climbed to his feet and looked around, trying to make since of where he was. "Where am I?" he asked to nobody in particular. he was surprised when he was answered.

 _ **"You Are in your mind's eye."**_ a distorted voice echoed around him, vibrating down to his very core.

"Who are you?" he stated bodly.

A black haze drifted lazily from between the trees and started to condense, a few feet in front of him, into a basic human shape. it then condensed more, creating more details, more shades, until it looked almost like Shinji, except for a few small details: it had pure, black hair and black eyes with red irises. " _ **I'm you."**_ It said, moving closer to Shinji arrogantly, _**"That is, the worst part of you."**_

Shinji stared at it. "What is your name then?"

It stopped, looking at the boy in confusion. And then it started laughing. _**"Ah, that's a good one. Never thought you'd ask that. My name is Sayomi, or at least that is what I think it is."**_

The corner of Shinji's lip rose slightly. "Night-Born, fitting." The Third-Child grinned, "So, tell me, why am I here?"

Sayomi clapped his hands and a table appeared along with a pair of chairs, _**"I pulled you here to tell you a few helpful things."**_ The Dark Being spread his hands. _**"I brought you here for two things: one, No matter what you do, you can't run from the past nor hide from the future; two, there is more than just you in this body."**_

Shinji looked up at him, "What do you mean?"

Sayomi started to fade away, _**"Oh, you know, just that in everybody there is the light, the dark and the inbetween. you of all people should know this."**_ Right before he faded away all together, he left one last piece of advice, _**"Just to let you know, Rei is not related to you in anyway, even before she was Reborn. Use that advice to your advantage. And tell Tabris I said hello when you see him again!"**_ He said with a smirk. Before the other boy could question what his other part said, the place around him faded into black, and he woke up for real this time.

He sat up with a gasp and he struggled to figure out what Sayomi had said about there being more than one being in his body. "Fuck." He exclaimed before climbing out of the bed and getting dressed in his school uniform.'I guess I should at least make Misato breakfast before I leave.' he thought as he exited his room and made his way to the kitchen. He cleared the table and pulled out the ingredients to make a bowl of a western style food called Rice Pudding, seemed interesting to say the least.

He sat the bowl of the table and yelled at his sleeping guardian. "I'm leaving for school, breakfast's on the table!"

He heard a groan come from Misato before he left, grabbing his small suitcase that contained his items before leaving. He shut the door behind him and made his way to school.

/Setting: School/

Shinji had entered the room and everybody ceased talking. The girl he recognized as the Class Representative and Hikari walked over to him. "Hello, you must be the new student, Right?" Shinji replied with a nod and Hikari continued. "Well, I'm the Class Rep. and my name is Hikari. Feel free to come to me if you have any problems. What's your name?"

The Third Child noticed the stares from his classmates. "I'm Shinji Ikari. It's nice to meet you."

"Well, Shinji, since there are plenty of empty seats, you can choose were to sit."

Shinji walked past her and straight to the girl he noticed sitting in her normal spot, the same spot she sat in in the past timeline. "It's nice to see you again, Rei." He greeted the blue-haired Angel. Toji quickly turned his head towards the pair.

"It's been a while, Shinji." Rei replied while standing up with a smile. She proceeded to enfold him in a hug and the class gasped.

"How do they know each other?"

"Never mind that, how did he get the Ice Queen to smile?"

"Who cares about that, They must know each other very well though."

Chatter echoed throughout the room and Shinji sat down in the seat beside Rei. he turned toward her. "it's nice to see you again though." He said before turning on his school laptop.

He opened up the chat while the teacher entered and had started the lesson, something about The Second Impact, or whatever? All Shinji knew was that it was something he already had heard, and something he knew the truth of considering he was an Angel and was given access to this Information.

^Hey, Rei, hows it been since you've came back?^ Shinji typed.

^Nothing Much, Only that I noticed the fight was shorter this time.^

^Can you come to NERV hospital later with me after this Angel Fight?^

^Sure^

The conversation carried on a little bit more until Shinji noticed the message from one of his classmates. He looked around, already knowing who sent it, but wanting to make sure. One of the girls smiled at him, and he read the message again.

^Are you the pilot? Y/N^

Shinji pondered if he should answer and then typed yes. The class erupted in noise and Shinji was surrounded by his fellow classmates.

"How did you become the pilot?"

"What were you fighting?"

"What are you piloting?"

A beeping noise emitted from Shinji's and Rei's phones a second before the sirens went off. "Time to leave Rei." he said before opening and jumping out of the window. That was two stories high. The students panicked and rushed to the window before sighing in relief when they saw Shinji and Rei running off hand in hand.

/

"The target has been captured optically. It has invaded the territorial waters."

"All hands to battle stations!" Fuyutsuki commanded the people below him, preparing for the Angel attack.

" Roger. Prepare for antiaircraft interception!"

" Tokyo-3 is transforming to the battle formation"

"House the central block!"

"The central block and District 1 to 7 have been housed."

"The notifications to the government and all ministries concerned have been finished."

"The present effective rate of the antiaircraft interception system is 48 %."

"What is the status of noncombatants and civilians?" Misato asked the technicians at their desks.

"It was reported that the evacuation has been finished." Shigeru answered.

/NERV Japan/

Shinji climbed into the entry plug and was inserted. "Where's the Angel at?" He questioned the technicians.

 _~In the center of the city, we're sending you up right behind it.~_

Shinji felt the all to familiar rush of gravity forcing him down into the cockpit as the EVA was launched upwards at mach speed. He quickly pulled the EVA off of the elevator when he reached the surface.

He was greeted by the sight of the worm like angel. It had a monstrous purple skin and glowing whips for arms.

 _ **'Shamshel - The Sun Of God'**_ He heard Sayomi echo in his mind as he rushed forward.

He rushed the Angel and had managed to cut off both whips and graze the core before he was thrown backwards onto the hill side, fingers barely missing his classmates.

/A few Minutes Earlier, NERV Shelter #5/

Toji: "Well, What is that?"

Kensuke: "I want to see that even only once until my death. "

Toji: "The battle above? "

Kensuke: "I'm afraid if the next enemy will come soon ... "

Toji: "Kensuke, what guy you are!"

Kensuke: "If I miss this chance, I might not forever ... Say, please help me to unlock the gate."

Toji: "If you go out, you'll be killed. "

Kensuke: "If we are here in the shelter, I wonder if we survive. Since I may be killed anyway, I want to see it before then."

Toji: "What a fool! What do you think Nerv exists for?! "

Kensuke: "What do you think the fighting machine of Nerv is?! The robot which the transferee pilots. At the last time, he protected us. If he doesn't want to pilot the robot, we all will be killed. You have an obligation to watch his battle, don't you?"

Toji: "There's no other choice. You are really faithful to your desires, aren't you?"

Kensuke started laughing.

/Current Time/

Shinji layed there in his EVA, flat on the hillside, remembering the past. "Misato, I'm letting them in!" Shinji yelled before ejecting the plug. "Get the fuck in!" he yelled at Toji and Kensuke. The duo scampered into the plug. The Entry Plug reinserted itself and started filling back up with LCL.

"Gah! What is this?!" Toji yelled, clutching his throat.

Kensuke almost cried as his camera was ruined by the liquid. "No! My Camera!"

Ritsuko was shocked less by what he had done and more at his sync rate. "How is this possible? Two foreign bodies are in the plug, the sync rate should be dropping, not staying the same!"

Shinji glared at the boys before resuming his tasks. "Shut up for now and let me do what I have to do." The two boys quieted and Shinji made the EVA stand up. "Time to finish what was started."

He grabbed the prog knife that had fell beside the EVA and ran to towards Shamshel. The Angel pierce Unit 01 in the Stomach and the arm causing Shinji to drop the knife. Shinji hissed in pain as he pushed forward, causing the newly regenerated whips to be forced further through the back of the EVA Unit. "I guess I'll just have to rip it out then." Shinji stated, grinning manically, baring his teeth, his eyes turning black with red corneas, not unlike Sayomi's.

Toji and kensuke had the nerve to be truly frightened at this display. Shinji propelled the EVA and started to rip out the core with extreme force. With a final heave, and a scream from Shamshel, he ripped the core out of the Angel and the body dissolved into a tidal wave of LCL. "Lunch Time." he proceeded to say before devouring the core, leaving a purple haired female in the EVA's palms. "Hey, Misato? Make sure someone's there for her." He said before collapsing due to blood loss.

The EVA powered down and Shinji collapsed. The Entry Plug ejected, causing Toji and Kensuke to cough up the orange Life Water and drag Shinji out of the plug. They pulled him over to the group of gathered people.

Misato started yelling at the duo. "Why where you two out of the shelters!?"

Kensuke started shaking, "We just wanted to watch him."

Misato sighed before motioning to a group of Section 2 agents, "Take them in and lock the up."

Shinji woke up for a short amount of time. "T-test them, they might be our next pilots." he shuddered before gaining unconsciousness again.

Misato sighed yet again. God, she'd started to hate her job.


	6. IMPORTANT ANNOUNCEMENTS

Hello, author here. It will be longer before my stories are updated due to my computer being broke amd typong on phones are hard as fuck.

Don't you worry cupcakes. I'll update as soon as I can.

Thanks for understanding.

Oh, Yeah. One last thing.

hellsink bathhall, Your one shot is about halfway finished. I'll have it uploaded within the week.


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